Fluid simulation only renders surface leaving cavities against domain
After giving this a bounty because I had the same problem, I found the solution. When you simulate the fluid, the default settings only simulate the surface layer of the liquid. This is called a narrow band, which reduces memory and computational power needed. For some reason, the fluid mesher only meshes the narrow band.
Scroll to the Liquid settings, and set narrow band to 0 to disable it.